Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: Empirical results and modeling challenges

Brajković, Vladimir; Pocrnic, Ivan; Kapš, Miroslav; Špehar, Marija; Cubric-Curik, Vlatka; Ristov, Strahil; Novosel, Dinko; Gorjanc, Gregor; Curik, Ino (2025) Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: Empirical results and modeling challenges. Journal of Dairy Science, 108 (1). pp. 664-678. ISSN 0022-0302

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Abstract

Substantial advances in livestock traits have been achieved primarily through selection strategies targeting variation in the nuclear genome, with little attention given to mitogenome variation. We analyzed the influence of the mitogenome on milk production traits of Holstein cattle in Croatia based on strategically generated next-generation sequencing data for 109 cows pedigree-linked to 7,115 milk production records (milk, fat, and protein yield) from 3,006 cows (first 5 lactations). Because little is known about the biology of the relationship between mitogenome variation and production traits, our quantitative genetic modeling was complex. Thus, the proportion of total variance explained by mitogenome inheritance was estimated using 5 different models: (1) a cytoplasmic model with maternal lineages (CYTO), (2) a haplotypic model with mitogenome sequences (HAPLO), (3) an amino acid model with unique amino acid sequences (AMINO), (4) an evolutionary model based on a phylogenetic analysis using Bayesian Evolutionary Analysis Sampling Trees phylogenetic analysis (EVOL), and (5) a mitogenome SNP model (SNPmt). The polygenic autosomal and X chromosome additive genetic effects based on pedigree were modeled, together with the effects of herd-year-season interaction, permanent environment, location, and age at first calving. The estimated proportions of phenotypic variance explained by mitogenome in 4 different models (CYTO, HAPLO, AMINO, and SNPmt) were found to be substantial given the size of mitogenome, ranging from 5% to 7% for all 3 milk traits. At the same time, a negligible proportion of the phenotypic variance was explained by mitogenome with the EVOL model. Similarly, in all models, no proportion of phenotypic variance was explained by the X chromosome. Although our results should be confirmed in other dairy cattle populations, including a large number of sequenced mitogenomes and nuclear genomes, the potential of utilizing mitogenome information in animal breeding is promising, especially as the acquisition of complete genome sequences becomes cost-effective.

Item Type:	Article
Uncontrolled Keywords:	Holstein cattlemilk production traitscomplete mitogenomenext-generation sequencingvariance components
Subjects:	BIOTECHNICAL SCIENCES > Agronomy > Genetics and Breeding of Plants, Animals and Microorganisms
Divisions:	Division of Electronics
Projects:	Project title Project leader Project code Project type Odgovor na inovacije u fenomici i genomici u oplemenjivanju mliječnih goveda Ino Čurik IP-2022-10-6914 HRZZ Upotreba cijelog genoma mitohondrijske DNA u oplemenjivanju i konzervacijskoj genetici goveda-MitoTAUROmics Ino Čurik IP-2013-11-9070 HRZZ
Depositing User:	Ivana Vuglec
Date Deposited:	26 Nov 2025 15:31
URI:	http://fulir.irb.hr/id/eprint/10090
DOI:	10.3168/jds.2024-25203

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